rs1800630

Variant names:

• chr6-31574699-C-A
• rs1800630

Your query was ambiguous. Multiple possible variants found:

• chr6-31574699-C-A
• chr6-31574699-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.144 in 151,842 control chromosomes in the GnomAD database, including 1,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

• Frequency: Genomes: 𝑓 0.14 (1698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: protective no assertion criteria provided B:1
• Conservation: PhyloP100: -2.77
• Publications: 551 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21898 AN: 151724 Hom.: 1699 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21905 AN: 151842 Hom.: 1698 Cov.: 31 AF XY: 0.146 AC XY: 10802 AN XY: 74186

African (AFR) AF: 0.109 AC: 4515 AN: 41394

American (AMR) AF: 0.139 AC: 2116 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3472

East Asian (EAS) AF: 0.161 AC: 827 AN: 5122

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4810

European-Finnish (FIN) AF: 0.162 AC: 1707 AN: 10550

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10581 AN: 67906

Other (OTH) AF: 0.163 AC: 344 AN: 2108

Alfa AF: 0.153 Hom.: 6769

Bravo AF: 0.141

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: protective

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Alzheimer disease, protection against (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.65
DANN	Benign	0.33
PhyloP100		-2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1800630; hg19: chr6-31542476;